7-28526023-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_182898.4(CREB5):​c.291+18286A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,046 control chromosomes in the GnomAD database, including 26,753 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.57 ( 26753 hom., cov: 32)

Consequence

CREB5
NM_182898.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.793
Variant links:
Genes affected
CREB5 (HGNC:16844): (cAMP responsive element binding protein 5) The product of this gene belongs to the CRE (cAMP response element)-binding protein family. Members of this family contain zinc-finger and bZIP DNA-binding domains. The encoded protein specifically binds to CRE as a homodimer or a heterodimer with c-Jun or CRE-BP1, and functions as a CRE-dependent trans-activator. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CREB5NM_182898.4 linkc.291+18286A>G intron_variant Intron 4 of 10 ENST00000357727.7 NP_878901.2 Q02930-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CREB5ENST00000357727.7 linkc.291+18286A>G intron_variant Intron 4 of 10 1 NM_182898.4 ENSP00000350359.2 Q02930-1

Frequencies

GnomAD3 genomes
AF:
0.574
AC:
87246
AN:
151928
Hom.:
26738
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.339
Gnomad AMI
AF:
0.614
Gnomad AMR
AF:
0.713
Gnomad ASJ
AF:
0.691
Gnomad EAS
AF:
0.719
Gnomad SAS
AF:
0.640
Gnomad FIN
AF:
0.724
Gnomad MID
AF:
0.661
Gnomad NFE
AF:
0.639
Gnomad OTH
AF:
0.600
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.574
AC:
87284
AN:
152046
Hom.:
26753
Cov.:
32
AF XY:
0.583
AC XY:
43312
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.339
Gnomad4 AMR
AF:
0.714
Gnomad4 ASJ
AF:
0.691
Gnomad4 EAS
AF:
0.720
Gnomad4 SAS
AF:
0.640
Gnomad4 FIN
AF:
0.724
Gnomad4 NFE
AF:
0.639
Gnomad4 OTH
AF:
0.600
Alfa
AF:
0.636
Hom.:
42206
Bravo
AF:
0.565
Asia WGS
AF:
0.650
AC:
2259
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
13
DANN
Benign
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs160346; hg19: chr7-28565641; API